Why is only the hair based particle system appearing in two levels of particles?
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Right Side Render.

Left Side Yellow Particles Emitter in Layer 1.  Group in Layer 2.  Brown Cube Reeds. Golden Seeds. Green Leaves.  Reeds, Seeds, Leaves are part of the emitter.  The [join] mesh command used.  

Nail Shaped Hair is the second Particles system of the reed emitter in Layer 2.  The Hair appears as strands in the 3D View Window.



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Second Emitter complex in layer 2.

Primary

You have already successfully rendered the emitter and the hair particle system.  I have done the same in a new file.  I have not succeeded to render the non hair non emitter.

You could have a finished model with only the group particles hair system present.  The seeds and leaves can be part of the emitter.

For the seed and leaves you can convert them to non particles and be part of the emitter. The particles system can be used to generate the model. Then press the button [convert] in the the modifier panel for the particle system.  The hair particles remain. The emitter is now a complex  of reed, leaves, seed.  Your artistic needs would determine if that is suitable. 

You do NOT need to convert hair.  The [convert] of the hair seems to produce edges only which will need to use something like a solidify modifier

Secondary

I used a particle instance modifier ... different from a particle system ... and I could duplicate hair but not object particles.

Tertiary

I will seek a few more alternatives.

Older

Verify your Object Cycles Setting, Cycles Ray Visibility: Camera checkbox is [enabled] for the missing particles.

Verify your particle systems camera render option is TRUE

Under the object Duplication Panel for the missing particles make sure the either None or Frames are selected.  Do not use Verts Faces Groups.

Verify all particles system generate particles for the frame above.

Verify that all materials are created for the render engine.  Cycles Render is compatible with Cycles materials.  Blender Render is compatible with Blender Materials.

Verify that the Render visibility is on for the missing materials.  The camera icon in the outliner panel.

Verify that you have no  transparency in your material.